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- PDB-4xvx: Crystal structure of an acyl-ACP dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4xvx
TitleCrystal structure of an acyl-ACP dehydrogenase
ComponentsAcyl-[acyl-carrier-protein] dehydrogenase MbtN
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / TB STRUCTURAL GENOMICS CONSORTIUM / TBSGC / ROSSMANN FOLD / ACYL-ACP BINDING / DEHYDROGENATION
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / catechol-containing siderophore biosynthetic process / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / flavin adenine dinucleotide binding
Similarity search - Function
Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain ...Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Acyl-[acyl-carrier-protein] dehydrogenase MbtN
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChai, A. / Johnston, J.M. / Bunker, R.D. / Lott, J.S. / Baker, E.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: A covalent adduct of MbtN, an acyl-ACP dehydrogenase from Mycobacterium tuberculosis, reveals an unusual acyl-binding pocket.
Authors: Chai, A.F. / Bulloch, E.M. / Evans, G.L. / Lott, J.S. / Baker, E.N. / Johnston, J.M.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 11, 2015ID: 4M6Z
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Jun 3, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
B: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0166
Polymers82,8332
Non-polymers2,1844
Water3,657203
1
A: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
B: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
hetero molecules

A: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
B: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,03312
Polymers165,6654
Non-polymers4,3688
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area26970 Å2
ΔGint-147 kcal/mol
Surface area47560 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-39 kcal/mol
Surface area28650 Å2
MethodPISA
3
A: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
hetero molecules

B: Acyl-[acyl-carrier-protein] dehydrogenase MbtN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0166
Polymers82,8332
Non-polymers2,1844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area8120 Å2
ΔGint-45 kcal/mol
Surface area29140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.104, 139.104, 253.093
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Acyl-[acyl-carrier-protein] dehydrogenase MbtN / Acyl-ACP dehydrogenase MbtN / Mycobactin synthase protein N


Mass: 41416.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: mbtN, fadE14, Rv1346, MTCY02B10.10 / Plasmid: PPROEXHTB / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P9WQF9, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#3: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23 % PEG 3350, 0.2 M DIAMMONIUM HYDROGEN CITRATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 17, 2010
RadiationMonochromator: SILICON DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 2.3→87.25 Å / Num. obs: 42053 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 39.86 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.821 / Mean I/σ(I) obs: 2.8 / % possible all: 96.5

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
MOLREPphasing
BUSTER2.11.5refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WS9

1ws9


Resolution: 2.3→58.6 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2118 5.04 %RANDOM
Rwork0.175 ---
obs0.176 42021 99.8 %-
Displacement parametersBiso mean: 43.63 Å2
Baniso -1Baniso -2Baniso -3
1--6.0116 Å20 Å20 Å2
2---6.0116 Å20 Å2
3---12.0233 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→58.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5595 0 145 203 5943
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0115850HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.077932HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2039SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes874HARMONIC5
X-RAY DIFFRACTIONt_it5850HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2322 175 5.69 %
Rwork0.2055 2902 -
all0.207 3077 -
obs--99.83 %

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